Subtype C infections in Africa

The past decade has seen a dramatic increase in the distribution of HIV-1 subtype C viruses, particularly in sub-Saharan Africa and especially the Southern region. To estimate the number of HIV-1 subtype C infections in African countries with C-viruses, the number of subtype C infections in each country was estimated using the subtype C sequence frequency and number of infected people for each country. The estimated number of subtype C infections compared with non-subtype C infections is shown in the maps below. When the number of non-subtype C infections (B) is subtracted from the total number of infections for each country (A), the remaining number of subtype C infections is seen to be the highest in Southern African countries where HIV prevalence is highest and subtype C is most predominant.  (see Table of prevalence).

History of subtype C: Epidemiology

The epidemic spread of HIV in sub-Saharan Africa began in the late 1970s and, during the late 1980s, gradually spread to the South of the continent. HIV-1 subtype C was first discovered in North East Africa in the early 1980s (1,2) and has since also moved to the southern parts of Africa. In addition, the subtype C epidemic has also spread to East and Central Africa where it is becoming the predominant subtype (3, 4, 5). The C epidemic has also spread to South and Central China, India and Brazil (6, 7, 8). The variants circulating in China are mainly B/C recombinants where the subtype C component appears to have been introduced into China from India (6).

The subtype C epidemic has now become the most predominant subtype in Southern African countries where HIV prevalence is the highest in the world. Extrapolating the subtype C sequence frequency from the Los Alamos sequence database shows that subtype C accounts for >46% of all infections in sub-Saharan Africa and contributes to just over 42% of global infections. Of all the new infections that occurred globally during the period from 1999 to 2002, 45% are estimated to be subtype C infections, based on the subtype C sequence frequency obtained from published data.  It is important to note that this estimate could be greater than the actual prevalence as a result of sequencing bias. However, there is still much evidence suggesting that subtype C is increasing and that there is a definite need to monitor and describe the viruses circulating in countries with high subtype C infections.


1. Salminen MO, Johansson B, Sonnerborg A, Ayehunnie S, Gotte D, Leinikki P, Burke DS, McCutchan FE. 1996. Full-length sequence of an Ethiopian human immunodeficiency virus type 1 (HIV-1) isolate of genetic subtype C. AIDS Res Hum Retroviruses. 12: 1329-39. [Medline]

2. McCormack GP, Glynn JR, Crampin AC, Sibande F, Mulawa D, Bliss L, Broadbent P, Abarca K, Ponnighaus JM, Fine PEM,? Clewley JP. 2002. Early evolution of the human immunodeficiency virus type 1 subtype C epidemic in rural Malawi. J. Virology 76 (24): 12890-99. [Medline]

3. Renjifo B, Chaplin B, Mwakagile D, Shah P, Vannberg F, Msamana G, Hunter D, Fawzi W, Essex M. 1998. Epidemic expansion of HIV type 1 subtype C and recombinant genotype in Tanzania. AIDS Res Hum Retroviruses. 4 (7): 635-8.

4. Neilson JR, John GC, Carr JK, Lewis P, Kreiss JK, Jackson S, Nduati RW, Mbori-Ngacha D, Panteleefe DD, Bodrug S, Giachetti C, Bott MA, Richardson BA, Bwayo J, Ndinya-Achola J, Overbaugh J. 1999. Subtype of human immunodeficiency virus type 1 and disease stage among women in Nairobi, Kenya. J Virology. 73 (5): 4393-4403. [Medline]

5. Vidal N, Peeters M, Mulanga-Kabeya C, Nzilambi N, Robertsons D, Ilunga W, Sema H, Tshimanga K, Bongo B, Delaporte E. 2000. Unprecedented degree o human immnunodeficiency virus type 1 (HIV-1) group M genetic diversity in Democratic Republic of Congo suggests that the HIV-1 pandemic originated in Central Africa. J Virology. 74 (22): 10498-507. [Medline]

6. Yu XF, Chen J, Shao Y, Beyrer C, Lai S. 1998. Two subtypes of HIV-1 among injection-drug users in southern China. Lancet. 351: 1250

7. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC. 1999. Full-length human immunodeficiency virus type 1 genomes from subtype C infected seroconverters in India, with evidence of intersubtype recombination. J Virology. 73 (1): 152-60

8. Soares MA, de Oliveira T, Brindeiro RM, Diaz RS, Sabino EC,? Brigido L, Pires IL, Morgado MC, Dantas MC, Barreira D, Teixeira PR, Cassol S, Tanuri A. 2003. A specific subtype C of human immunodeficiency virus type 1 circulates in Brazil. AIDS 17: 11-21. [Medline]

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